Syntax Tree is a suite of tools built on top of the internal CRuby parser. It provides the ability to generate a syntax tree from source, as well as the tools necessary to inspect and manipulate that syntax tree. It can be used to build formatters, linters, language servers, and more.

This package provides a package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.

The spatialHeatmap package offers the primary functionality for visualizing cell-, tissue- and organ-specific assay data in spatial anatomical images. Additionally, it provides extended functionalities for large-scale data mining routines and co-visualizing bulk and single-cell data. A description of the project is available here: https://spatialheatmap.org.

Implementation of the Marine Predators Algorithm (MPA) in R. MPA is a nature-inspired optimization algorithm that follows the rules governing optimal foraging strategy and encounter rate policy between predator and prey in marine ecosystems. Based on the paper by Faramarzi et al. (2020) <doi:10.1016/j.eswa.2020.113377>.

Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornsteinâ Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.

This package provides a collection of sample datasets on various fields such as automotive performance and safety data to historical demographics and socioeconomic indicators, as well as recreational data. It serves as a resource for researchers and analysts seeking to perform analyses and derive insights from classic data sets in R.

Create beautifully color-coordinated and customized themes for your xaringan slides, without writing any CSS. Complete your slide theme with ggplot2 themes that match the font and colors used in your slides. Customized styles can be created directly in your slides R Markdown source file or in a separate external script.

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

REDUCE IDE is an Emacs package that provides an Integrated Development Environment for the REDUCE computer algebra system within the GNU Emacs editor. Its two major components are Emacs Lisp libraries that provide major modes for editing REDUCE source code and running a command-line version of REDUCE in an Emacs window.

Distributional instrumental variable (DIV) model for estimation of the interventional distribution of the outcome Y under a do intervention on the treatment X. Instruments, predictors and targets can be univariate or multivariate. Functionality includes estimation of the (conditional) interventional mean and quantiles, as well as sampling from the fitted (conditional) interventional distribution.

An information-theoretic diagnostic technique for estimating the intrinsic dimensionality of tabular datasets. Evaluates shared probability mass via a transformed mutual information metric. Aims to extract the Intrinsic Generative Rank (r) and structural topology. For full methodological details, see the preprint by Lee-St. John (2026) <https://zenodo.org/records/22028087>.

An easy tool to transform 2D longitudinal data into 3D arrays suitable for Long short-term memory neural networks training. The array output can be used by the keras package. Long short-term memory neural networks are described in: Hochreiter, S., & Schmidhuber, J. (1997) <doi:10.1162/neco.1997.9.8.1735>.

The d3.js framework with the plugins d3-voronoi-map, d3-voronoi-treemap and d3-weighted-voronoi are used to generate Voronoi treemaps in R and in a shiny application. The computation of the Voronoi treemaps are based on Nocaj and Brandes (2012) <doi:10.1111/j.1467-8659.2012.03078.x>.

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

Calculates and visualises speech rhythm and timing metrics. The rhythm.metrics package provides a standardised workflow to compute common metrics including Delta C, Delta V, VarcoC, VarcoV, the percentage of vocalic intervals (%V), and both raw and normalised Pairwise Variability Indices (rPVI, nPVI). It includes functions for calculating and visualising these measures to facilitate cross-linguistic and developmental rhythm research. Delta C, Delta V, and %V measures are based on Ramus et al. (1999) <doi:10.1016/S0010-0277(99)00058-X>; VarcoC and VarcoV measures are based on Dellwo (2006, ISBN: 9783631554777); and rPVI-C and nPVI-V are based on Grabe & Low (2002) <doi:10.1515/9783110197105.2.515>.

This is a package for saving Bioconductor data structures into file artifacts, and loading them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Text::Hyphen is a Ruby library to hyphenate words in various languages using Ruby-fied versions of TeX hyphenation patterns. It will properly hyphenate various words according to the rules of the language the word is written in. The algorithm is based on that of the TeX typesetting system by Donald E. Knuth.

This package provides a streamlined and user-friendly framework for bootstrapping in state space models, particularly when the number of subjects/units (n) exceeds one, a scenario commonly encountered in social and behavioral sciences. The parametric bootstrap implemented here was developed and applied in Pesigan, Russell, and Chow (2025) <doi:10.1037/met0000779>.

Last Resort is a special-purpose font intended as a user-friendly alternative to tofu symbols. It includes glyphs designed to allow users to recognize which Unicode block a character belongs to so they can identify what type of font to install to properly display text. Undefined code points and noncharacters are also represented.

An interface to the table storage service in Azure': <https://azure.microsoft.com/en-us/services/storage/tables/>. Supplies functionality for reading and writing data stored in tables, both as part of a storage account and from a CosmosDB database with the table service API. Part of the AzureR family of packages.

Reads several formats of 13C data (IRIS/Wagner, BreathID) and CSV. Creates artificial sample data for testing. Fits Maes/Ghoos, Bluck-Coward self-correcting formula using nls', nlme'. Methods to fit breath test curves with Bayesian Stan methods are refactored to package breathteststan'. For a Shiny GUI, see package dmenne/breathtestshiny on github.

Enables simulation of water piping networks using EPANET'. The package provides functions from the EPANET programmer's toolkit as R functions so that basic or customized simulations can be carried out from R. The package uses EPANET version 2.2 from Open Water Analytics <https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.2>.

Econometric analysis of multiple-input-multiple-output production technologies with ray-based input distance functions as suggested by Price and Henningsen (2023): "A Ray-Based Input Distance Function to Model Zero-Valued Output Quantities: Derivation and an Empirical Application", Journal of Productivity Analysis 60, p. 179-188, <doi:10.1007/s11123-023-00684-1>.

This package provides a generalization of the statistic used in Friedman's ANOVA method and in Durbin's rank test. This nonparametric statistical test is useful for the data obtained from block designs with missing observations occurring randomly. A resulting p-value is based on the chi-squared distribution and Monte Carlo method.